Roychowdhury Tanmoy, Vishnoi Anchal, Bhattacharya Alok
School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi.
Sci Rep. 2013;3:2634. doi: 10.1038/srep02634.
Whole genome sequences are ideally suited for deriving evolutionary relationship among organisms. With the availability of Next Generation sequencing (NGS) datasets in an unprecedented scale, it will be highly desirable if phylogenetic analysis can be carried out using short read NGS data. We described here an anchor based approach NexABP for phylogenetic construction of closely related strains/isolates from NGS data. This approach can be used even in the absence of a fully assembled reference genome and works by reducing the complexity of the datasets without compromising results. NexABP was used for constructing phylogeny of different strains of some of the common pathogens, such as Mycobacterium tuberculosis, Vibrio cholera and Escherichia coli. In addition to classification into distinct lineages, NexABP could resolve inner branches and also allow statistical testing using bootstrap analysis. We believe that there are some clear advantages of using NexABP based phylogenetic analysis as compared to other methods.
全基因组序列非常适合用于推导生物体之间的进化关系。随着前所未有的大规模下一代测序（NGS）数据集的出现，如果能够使用短读长NGS数据进行系统发育分析，那将是非常理想的。我们在此描述了一种基于锚定的方法NexABP，用于从NGS数据构建密切相关菌株/分离株的系统发育。即使在没有完全组装好的参考基因组的情况下，这种方法也可以使用，其工作原理是在不影响结果的情况下降低数据集的复杂性。NexABP被用于构建一些常见病原体（如结核分枝杆菌、霍乱弧菌和大肠杆菌）不同菌株的系统发育。除了分类到不同的谱系外，NexABP还可以解析内部分支，并且还允许使用自展分析进行统计检验。我们认为，与其他方法相比，使用基于NexABP的系统发育分析有一些明显的优势。
